Table 2.
Functional enrichment analysis of the DEGs in different transcriptomes by the DAVID functional annotation clustering tool
| Comparison | Tissue | Up-regulated | Representative annotation terms | Enrichment score | Genes |
|---|---|---|---|---|---|
| A | cEB vs. cLB | cEB | Translation | 11.57 | COG8, RPL22, HARS, RPL19, RPL10A, YARS, DENR, RPS14, RPS4, MRPL16, RPL13, MRPL23, RPL30, MRPL2, RPL18A, RPS8, RPL37A, RPSA, MRPL24, RPS15, EEF1D, RPLP1, RPL8, RPS7, RPL31, RPL17, MRPS12, RPLP0, RPS28 |
| Oxidative phosphorylation | 2.99 | NDUFA2, UQCR11, NDUFA8, ATP5A1W, NDUFB6, NDUFS5, PPA1, COX4I1, NDUFAB1, UQCRQ, COX6A1, COX15, ATP5H, UQCR10, NDUFB3, NDUFA1, NDUFS6, COX8A, COX5A, ATP5O, UQCRH, COX6C, NDUFA11 | |||
| Hydrogen ion transmembrane transporter activity | 2.78 | ATP5A1W, ATP5O, COX4I1, COX6C, COX5A, LOC770937, UQCRH, UQCRQ | |||
| Pyrimidine metabolism | 1.61 | NME2, ITPA, POLR2L, POLR2H, POLR1C, CANT1, POLR3H, RPB6 | |||
| Contractile fiber part | 1.37 | MYL4, TNNC1, HSPB1, CRYAB | |||
| Ribosomal subunit | 1.24 | RPL19, RPS14, RPSA, RPS15, RPL17, MRPS12 | |||
| Peptidyl-prolyl cis-trans isomerase activity | 1.22 | PPIB, FKBP25, FKBP1B | |||
| Inorganic cation transmembrane transporter activity | 1.10 | ATP5A1W, COX4I1, UQCRQ, UQCR10, RHBG, COX5A, ATP5O, UQCRH, COX6C | |||
| cLB | Amino acid transmembrane transporter activity | 2.33 | SLC38A2, SLC6A6, SLC7A5, SLC7A11 | ||
| Transmembrane | 1.72 | ATP1B3, ELOVL6, ST8SIA5, BMPR2, EGFR, FZD10, GJA1, ITGA6, ITGAV, LAMP2, NRP1, SLC2A1, SLC38A2, SLC6A6, SLC7A5, SCD, TSPAN18, TFRC, TMEM41B, TYR | |||
| Lysosome | 1.64 | LAPTM5, CTSD, ARL8A, LAMP2 | |||
| Tube development | 1.43 | SP3, NRP1, EPAS1, TP63, BMPR-II, BMPR1A | |||
| Enzyme linked receptor protein signaling pathway | 1.33 | SMAD5, MADH2, BMPR1A, NRP1, BMPR-II, EGFR | |||
| Carboxylic acid biosynthetic process | 1.22 | SCD, QKI, ELOVL6, CBS | |||
| Plasma membrane | 1.15 | LAPTM5, BMPR1A, ITGAV, TJP1, SLC2A1, SLC6A6, BMPR-II, SLC38A2, LAMP2, ITGA6, QKI, EGFR, GJA1, PANX1, DSC1 | |||
| B | cEB vs. cEF | cEB | Translation | 20.68 | RPL22, HARS, RPL35, RPL19, MRPL17, RPL10A, RPL27, RPL26, YARS, DENR, RPS14, RPL6, RPS4, RPS24, MRPL16, EF1A, RPL27A, RPL13, MRPL23, MRPS11, RPL4, RPS27A, EIF3J, RPL30, MRPL2, RPL18A, RPS8, RPL14, RPSA, RPL3, MRPL24, RPL37, RPS15, EEF1D, RPLP1, RPL8, RPS7, RPL31, RPS3, MRPS12, RPLP0, RPS28, COG8, RPL17 |
| Oxidative phosphorylation | 3.83 | NDUFA2, UQCR11, NDUFA8, ATP5A1W, NDUFB6, NDUFS5, COX4I1, NDUFAB1, COX6A1, COX15, ATP5H, UQCR10, NDUFB3, NDUFA1, NDUFB5, NDUFS6, COX5A, UQCRH, COX6C, ATP5B, ATP5G1, UQCRQ, COX7B, COX8A, ATP5O, NDUFA11 | |||
| Ribosomal subunit | 3.39 | RPL19, RPL26, RPS14, RPS27A, RPSA, RPS15, RPS3, DAP3, MRPS12, RPL17 | |||
| Pyrimidine metabolism | 2.07 | POLR2C, NME2, ITPA, POLR2L, POLR1D, POLR2H, POLR1C, CANT1, RPB6, POLR2I | |||
| Ubiquinol-cytochrome-c reductase activity | 2.00 | UQCRH, UQCR10, UQCRQ | |||
| RNA polymerase | 1.36 | POLR2H, RPB6, POLR1D, POLR2I, POLR1C, POLR2L, POLR2C | |||
| Transmembrance | 2.76 | ATP1A1, ATP1B3, EPHB6, FAT, GPR177, ST8SIA5, ACVR1, CXCR7, EGFR, FGFR2, FGFR3, FZD10,GJA1, ITGA6, ITGAV, LAMP2, LAPTM4A, PTPLAD1, SLC22A5, SLC16A9, SLC2A1, SLC26A5, SLC39A13, SLC6A6, SLC7A5, SCD, SDC3, TSPAN18, TMEM121, TMEM175, TMEM41B, TYR, TYRP1 | |||
| cEF | Tissue morphogenesis | 1.59 | PRKAR1A, LMO4, TP63, TWSG1, JAG1, FGFR2, ACVR1, CA2 | ||
| Regulation of ossification | 1.58 | SMAD5, JAG1, FGFR2, HIF1A, ACVR1, WNT7B | |||
| Ossification | 1.28 | SMAD5, TWSG1, FGFR2, MGP | |||
| Carboxylic acid transport | 1.25 | SLC7A5, SLC6A6, SLC7A11, PLIN2 | |||
| Glycoprotein metabolic process | 1.18 | ST8SIA5, B3GNT5, B3GALNT1, HIF1A, B3GNT9 | |||
| Transmembrane receptor protein serine/threonine kinase signaling pathway | 1.13 | SMAD5, TWSG1, ACVR1, MADH2 | |||
| Enzyme linked receptor protein signaling pathway | 1.13 | EPHB6, JAK1, SMAD2, ACVR1, EGFR, FGFR2, FGFR3, RHOQ, SMAD5, TWSG1, | |||
| C | cEF vs. cMF | cEF | Skeletal system development | 2.81 | MGP, GLI1, WWOX, IGFBP5, GJA5, SHH, SOX14, SMAD1, CBFB |
| Signal peptide | 2.29 | KITLG, NELL2, ADCYAP1, AGRN, APOA1, CTSD, CHRNA4, CRH, FMOD, FZD10, FRZB, IGFBP2, MGP, MXRA8, NFASC, NPY, PON2, PLTP, SFRP2, SEMA3A, SILV, SHH, TTR, TSKU, TYR, TYRP1, KIT | |||
| Tube development | 1.62 | WNT5A, LMO4, LIPA, SHH, EDNRA, RARB, GJA5, CRH, GLI1 | |||
| Melanin biosynthetic process | 1.53 | TYR, TYRP1, PMEL | |||
| Drug metabolism | 1.48 | GSTO1, GSTA, MGST2, ALDH3B1 | |||
| Lytic vacuole | 1.38 | CTSD, NAGA, CTSL2, SLC48A1 | |||
| Developmental protein | 1.38 | LFNG, BASP1, FZD10, FRZB, GLI1, MGP, MSX1, SFRP2, SEMA3A, SHH, TSKU, WNT2B, WNT5A | |||
| Regulation of transcription, DNA-dependent | 1.26 | PKNOX2, POU2F3, SMAD1, SMAD2, SOX10, SOX14, AGRN, CBFB, DLX6, FOXI3, GLI1, HMGA2, MED22, MSX1, RHOQ, RBBP7, RARB, LOC425662, IRX5, SHH, THRB, TCEA2, TFAP2B, MYCL1, MYCN | |||
| Respiratory tube development | 1.23 | WNT5A, LIPA, SHH, CRH, GLI1 | |||
| cMF | Extracellular region | 7.81 | HBEGF, COL3A1, STC2, CTGF, SS2, FN1, MMP2, ANXA2, QSOX1, SPARC, LAMC2, ST6GAL1, DKK3, ADIPOQ, ADM, COL6A1, GPC4, COL6A2, JSC, CD44, MDK, CYR61, SERPINI1, COL1A2, EREG, THBS2, LUM, IGFBP7, APOLD1, EPDR1, PLA2G12A, INHBA, LGALS1, TIMP3, FBLN1, LAMA3, COL8A1, ADAMTS1, CD109, NOV, COL4A1, COL4A2, OSF-2, AVD, ENSGALG00000016682, ENSGALG00000011930 | ||
| Carbohydrate binding | 2.99 | MRC2, HBEGF, CTGF, FN1, LAMC2, CD44, MDK, THBS2, CLEC3B, LGALS1, OSF-2 | |||
| Signal peptide | 2.62 | CD3E, GFRA4, K123, TIMP3, CDH5, COL1A2, COL3A1, COL6A1, COL6A2, COL8A1, CTGF, CYR61, DKK3, FBLN1, INHBA, ITGA6, LEPREL1, LUM, MMP2, LOC769899, MDK, PTGS2, QSOX1, SPARC, SERPINI1, SDK2, NOV, THBS2 | |||
| Cell adhesion | 2.25 | ITGB3, PPARD, CTGF, FN1, SDK2, CDH5, COL6A1, COL6A2, CD44, ITGA6, THBS2, EPDR1, COL8A1, EDIL3, OSF-2 | |||
| Vasculature development | 2.17 | CTGF, PRRX1, MMP2, ANXA2, CDH5, CYR61, CAV1, COL1A2, EPAS1, MYH9 | |||
| Collagen | 2.12 | ADIPOQ, COL1A2, COL3A1, COL4A1, COL6A1, COL6A2, COL8A1, | |||
| Phospholipid binding | 1.50 | ANXA1, ANXA2, ANXA5 | |||
| Vascular smooth muscle contraction | 1.85 | ADRA1A, ITPR3, PLA2G4A, ACTG2, ARHGEF12, PLCB4, PLA2G12A, ITPR2, PLA2G10, RAMP2, PLA2G4C | |||
| Cell-substrate adhesion | 1.40 | ITGB3, PPARD, CTGF, FN1, ITGA6, EPDR1 | |||
| Regulation of cell growth | 1.34 | CTGF, BCL6, CYR61, IGFBP7, INHBA, NOV | |||
| Cell surface | 1.03 | ITGB3, HSPB1, II, CD3E, CD44, MDK, ITGA6 | |||
| D | cMF vs. cLF | cMF | Secondary metabolic process | 2.33 | PMEL, TYRP1, ALDOB, TYR |
| Organic acid transport | 2.16 | SLC6A6, CD36, PLIN2, OCA2 | |||
| Signal peptide | 1.53 | C1ORF187, FZD10, GSN, LY75, LOC769899, MDK, NPY, OVM, PLTP, QSOX1, SOSTDC1, SILV, SHH, TYR, TYRP1, KIT | |||
| cLF | Extracellular region part | 5.09 | HBEGF, LAMB3, COL5A2, COL5A1, CTGF, FN1, SPARC, LAMC2, ADIPOQ, OSTN, LAMB1, THBS1, INHBA, LAMA3, COL12A1, COL4A1, OSF-2, MMP27, COL1A1, OVOS2 | ||
| Structural molecule activity | 3.43 | LOC395532, COL4A1, COL5A1, COL5A2, COL7A1, LOC395906, NEFL, RPL36, LOC771066, THBS1 | |||
| Blood vessel development | 2.47 | THY1, CDH2, CAV1, COL5A1, CTGF, THBS1 | |||
| Glycoprotein | 2.09 | ST6GALNAC2, ST6GAL1, THY1, ADORA1, ALPL, LOC395532, CDH2, CHST3, ENSGALG00000015908, FN1, HSP90B1, INHBA, LAMB1, NTM, P4HA2, SPARC, SERPINH1, MOXD1 | |||
| Regulation of cell migration | 1.98 | THY1, ADORA1, HBEGF, THBS1, LAMA3 | |||
| Calcium binding | 1.31 | ACTN1, CDH2, CALM1, SPARC, TNNC1 | |||
| Glycoprotein biosynthetic process | 1.31 | ST6GALNAC2, ST3GAL2, ST6GAL1, B3GNT2, GALNT1, CHST3 | |||
| Cell adhesion | 1.30 | THY1, NTM, COL5A1, COL7A1,CTGF, FN1, LAMB1, THBS1, CDH2, DSG2, EDIL3, POSTN | |||
| Negative regulation of molecular function | 1.26 | THY1, ENSGALG00000014471, CAV1, HSPA5 | |||
| Endoplasmic reticulum | 1.22 | HSPA5, MOXD1, ITPR3, ADIPOQ, P4HA2, THY1, CAV1, SERPINH1, HSP90B1, DUOXA1 | |||
| Identical protein binding | 1.20 | TNNC1, HSPB1, ADIPOQ, INHBA, CAT, MTMR2 | |||
| Regulation of cellular protein metabolic process | 1.11 | ADIPOQ, PACSIN3, CAV1, THBS1NN BDKRB2 |
The genes were analyzed by the Functional Annotation Clustering Tool. The top annotation clusters that had group enrichment scores greater than 1 were listed. The representative biology terms associated with the top annotation clusters are manually summarized